Ted Brookings
Ted Brookings
* Added MinGqVariantFilterBase * * loads VCF, pedigree, UCSC genome tract, and truth data * * calculates variant overlap with genome tracts * * forms matrices, tensors, and other helping...
This is related to issue #174 and is a solution suggested in that thread. It would empower terser more maintainable WDLs if we could check if a map has a...
I have a WDL (with `version 1.1` at the top). I'm executing `miniwdl check` with version 1.11.1. In my task I have an array of simple structs that I need...
In the interest of time, some reviewer comments were left unaddressed in [PR 373](https://github.com/broadinstitute/gatk-sv/pull/373) I attempted to address all the comments that were straightforward and would not affect the basic...
## Minor refactoring A regression introduced in bcftools version 1.14 caused the SingleSampleFiltering.wdl task FilterVcfBySampleGenotypeAndAddEvidenceAnnotation to fail. I made a work-around using awk, but once that regression is addressed, the...
## Minor refactor Once the PR to decrease the number of docker images is accepted, there will be redundant references to the sv_pipeline docker in terms of the old dockers...
At least some fulcrum projects use Multiprocessing with Queues for parallel processing. e.g. ``` tasks = [ ( _function_to_process_in_parallel, (task_argument, general_arg1, general_arg2), # note: kwargs are not possible ) for...
Add capability to precisely control thickness, color, and dash of table cell borders. `TableBordersLayout` is changed from an enum to a more complex class with helper style classes that allow...
Adds a tool to downsample VCFs based on allele depths. Currently only handles biallelic variants.
I'm working in a genome with a large number of small scaffolds. In a cohort with 767 samples, on one of the scaffolds 106 of the samples have no informative...